The investigation, to see whether the US software giant is "abusing and defending its market position" through the practice, comes as computer users have massively adopted online virtual meetings since the coronavirus pandemic.
"Remote communication and collaboration tools like Teams have become indispensable for many businesses in Europe," the commission's antitrust chief Margrethe Vestager, said.
"We must therefore ensure that the markets for these products remain competitive, and companies are free to choose the products that best meet their needs," she said.
Teams is a platform that allows users to communicate through messages, video calls and file sharing. Rival communications platforms include Zoom, Google Meet, and Cisco Webex.
Microsoft bundles Teams with its cloud-based Office 365 and Microsoft 365 suites.
The commission said that the shift to cloud-based platforms and apps has allowed more players to enter the market, and noted that such software is usually subscription-based, locking users in the long term.
It underlined that the Microsoft cloud-based suites were "well-entrenched", and bundling Teams with them could be "restricting competition" in Europe.
"The Commission is concerned that Microsoft may grant Teams a distribution advantage by not giving customers the choice on whether or not to include access to that product when they subscribe to their productivity suites and may have limited the interoperability between its productivity suites and competing offerings," its statement said.
"These practices may constitute anti-competitive tying or bundling and prevent suppliers of other communication and collaboration tools from competing."
A Microsoft spokesperson said: "We respect the European Commission's work on this case and take our own responsibilities very seriously. We will continue to cooperate with the Commission and remain committed to finding solutions that will address its concerns."